GATK Germline CNV Discovery
This is just an exploratory question for my understanding.
How GATK's germline CNV calling works in single sample mode vs cohort mode?
Have you seen this document about GermlineCNVCaller and the difference between CASE and COHORT modes? I am going to move your post to the General Discussion topic as the Germline topic is for reporting bugs and issues with GATK.
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